DatabaseDocument.java

  {
    int i = 0;

    try
    {
      
      ChadoDAO dao = getDAO();
      boolean unchanged;
      
      //
      // check feature timestamps have not changed
      Vector names_checked = new Vector();
      for(i = 0; i < sql.size(); i++)
      {
        ChadoTransaction tsn = (ChadoTransaction) sql.get(i);
 
        if(tsn.getType() != ChadoTransaction.INSERT_FEATURE ||
           tsn.getType() != ChadoTransaction.DELETE_FEATURE)
        {
          final List uniquename = tsn.getUniquename();
          
          for(int j=0; j<uniquename.size(); j++)
          {
            if(names_checked.contains((String)uniquename.get(j)))
              continue;
            
            names_checked.add((String)uniquename.get(j));
            unchanged = checkFeatureTimestamp(schema, 
                           (String)uniquename.get(j), 
                         tsn.getLastModified(), dao);
            if(!unchanged)
              return 0;
          }
        }
      }  
      
      try
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).startTransaction();

        //
        // commit to database
        for(i = 0; i < sql.size(); i++)
        {
          ChadoTransaction tsn = (ChadoTransaction) sql.get(i);

          if(tsn.getType() == ChadoTransaction.UPDATE)
            dao.updateAttributes(tsn);
          else if(tsn.getType() == ChadoTransaction.INSERT)
            dao.insertAttributes(tsn);
          else if(tsn.getType() == ChadoTransaction.DELETE)
            dao.deleteAttributes(tsn);
          else if(tsn.getType() == ChadoTransaction.INSERT_FEATURE)
            dao.insertFeature(tsn, feature_id);
          else if(tsn.getType() == ChadoTransaction.DELETE_FEATURE)
            dao.deleteFeature(tsn);
          else if(tsn.getType() == ChadoTransaction.DELETE_DBXREF)
            dao.deleteFeatureDbxref(tsn);
          else if(tsn.getType() == ChadoTransaction.INSERT_DBXREF)
            dao.insertFeatureDbxref(tsn);
          else if(tsn.getType() == ChadoTransaction.DELETE_ALIAS)
            dao.deleteFeatureAlias(tsn);
          else if(tsn.getType() == ChadoTransaction.INSERT_ALIAS)
            dao.insertFeatureAlias(tsn);
          else if(tsn.getType() == ChadoTransaction.UPDATE_FEATURE_RELATIONSHIP)
            dao.updateFeatureRelationshipsForSubjectId(tsn);
        }

        //
        // update timelastmodified timestamp
        Timestamp ts = null;
        Timestamp ts2;
        names_checked = new Vector();
        for(int j = 0; j < sql.size(); j++)
        {
          ChadoTransaction tsn = (ChadoTransaction) sql.get(j);

          if(tsn.getType() != ChadoTransaction.INSERT_FEATURE &&
             tsn.getType() != ChadoTransaction.DELETE_FEATURE)
          {
            final List uniquename = tsn.getUniquename();

            // update timelastmodified timestamp
            for(int k = 0; k < uniquename.size(); k++)
            {
              if(names_checked.contains((String) uniquename.get(k)))
                continue;

              names_checked.add((String) uniquename.get(k));

              dao.writeTimeLastModified((String) uniquename.get(k), ts);
              ts2 = dao.getTimeLastModified((String) uniquename.get(k));
              if(ts2 == null)
                continue;

              if(ts == null)
                ts = ts2;

              GFFStreamFeature gff_feature = (GFFStreamFeature) tsn
                  .getFeatureObject();
              
              gff_feature.setLastModified(ts);
            }
          }
        }
        
        if(dao instanceof IBatisDAO && 
           System.getProperty("nocommit") == null)
           ((IBatisDAO) dao).commitTransaction();
      }
      finally
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).endTransaction();
      }
    }
    catch (java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "Problems Writing...\n" +
                                    sqlExp.getMessage(),
                                    "Problems Writing to Database ",
                                    JOptionPane.ERROR_MESSAGE);
      sqlExp.printStackTrace();
    }
    catch (java.net.ConnectException conn_ex)
    {
      JOptionPane.showMessageDialog(null, "Problems connecting..."+
                                    conn_ex.getMessage(),
                                    "Database Connection Error - Check Server",
                                    JOptionPane.ERROR_MESSAGE);
      conn_ex.printStackTrace();
    }

      
    return i;
  }
  
  /**
   * Check the <code>Timestamp</code> on a feature (for versioning).
   * @param schema      the schema
   * @param uniquename  the feature uniquename
   * @param timestamp   the last read feature timestamp
   * @throws SQLException
   */
  public boolean checkFeatureTimestamp(final String schema,
                                       final String uniquename,
                                       final Timestamp timestamp,
                                       final ChadoDAO dao)
                                       throws SQLException
  {
    Timestamp now = dao.getTimeLastModified(uniquename);
    
    if(now != null && timestamp != null)
    {
      now.setNanos(0);
      timestamp.setNanos(0);
      
      if(now.compareTo(timestamp) != 0)
      {
        SimpleDateFormat date_format = 
                   new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
        
        //System.out.println(date_format.format(now)+"   "+
        //                   date_format.format(timestamp));
        int select = JOptionPane.showConfirmDialog(null, uniquename +
                                      " has been altered at :\n"+
                                      date_format.format(now)+"\nOverwite?", 
                                      "Feature Changed", 
                                      JOptionPane.OK_CANCEL_OPTION);
        if(select == JOptionPane.OK_OPTION)
          return true;
        else
          return false;
      }
    }
    return true;
  }

  public static void main(String args[])
  {
    try
    {
      ChadoDAO dao;
      DatabaseEntrySource src = new DatabaseEntrySource();
      src.setLocation(true);
      
      if(System.getProperty("ibatis") == null)
        dao = new JdbcDAO(src.getLocation(), src.getPfield()); 
      else
        dao = new IBatisDAO(src.getPfield());
      
      ChadoFeature feature = new ChadoFeature();
      feature.setUniquename(args[0]);
      List schemas = new Vector();
      schemas.add(args[1]);
      List featureList = dao.getLazyFeature(feature); 
      System.out.println("FINISHED getFeature()");
      for(int i = 0; i < featureList.size(); i++)
      {
        feature = (ChadoFeature)featureList.get(i);
        
        String abb  = feature.getOrganism().getAbbreviation();
        String type = feature.getCvterm().getName();
        int fmin    = feature.getFeatureloc().getFmin() + 1;
        int fmax    = feature.getFeatureloc().getFmax();
        String featprop = 
          ((ChadoFeatureProp)feature.getFeaturepropList().get(0)).getCvterm().getName();
        
        System.out.print(fmin+".."+fmax);
        System.out.print(" "+type);
        System.out.print(" "+featprop);
        System.out.print(" "+feature.getFeatureloc().getStrand());
        System.out.print(" "+feature.getUniquename());
        System.out.print(" "+abb);
        System.out.println(" "+Integer.toString(feature.getId()));
        
        Hashtable synonyms   = dao.getAlias(feature.getUniquename());
        Vector syns = (Vector)synonyms.get(new Integer(feature.getId()));
        for(int j=0; j<syns.size(); j++)
        {
          ChadoFeatureSynonym alias = (ChadoFeatureSynonym)syns.get(j);
          System.out.print(" "+alias.getSynonym().getCvterm().getName()+
                           "="+alias.getSynonym().getName());
        }
        
        System.out.println(" "); 
      }
    }
    catch(SQLException sqle)
    {
      sqle.printStackTrace();
    }
    catch(ConnectException e)
    {
      e.printStackTrace();
    }
  }

  public Document getParent()
  {
    return null;
  }
}